We'd like to stay in Peru for about 3 week this September. We're interested in visiting the Amazonian jungles, mostly for the wildlife, I care mostly about seeing monkeys, dolphins and other bigger animals, but seeing the mighty river itself also sound very appealing. From all I've read, Iquitos sounds like a much more interesting place on its own, but everyone says wildlife is better in the south. Now, my question here is: for the animals I've mentioned, is Puerto Maldonado a clear winner or can I still see it all around Iquitos as well? Also, is there a point in seeing both during a 3-week trip? I presume there isn't, but better to ask...
I'll note up front that I've only been to Puerto Maldonado of the two, but of your interests you've listed:
- While Puerto Maldonado is on the Rio Madre de Dios, Iquitos is on the Amazon River proper. At Iquitos it is already at least three times the size of Rio Madre de Dios. Advantage: Iquitos.
- Monkeys are visible at both, but the river dolphins are only present at Iquitos. Advantage: Iquitos.
You won't be spending much time in Puerto Maldonado proper if you do visit, as presumably you would be staying in lodges in the jungle. There is not much in town.
While wildlife might be "better" (an admittedly subjective term) around Puerto Maldonado, it is still largely luck of the draw. The only large non-aquatic animals we saw in half a week were capybara, though we were taken to a family of river otters as well as spotting a caiman.
Overall I would suggest opting for Iquitos based off my and others' anecdotal evidence and your priorities, but with a caveat that if you are willing to spend the time and money to travel up to Manu National Park you may receive a different experience to our's.
I have quite a bit South American experience though, in fairness, not too much Amazonian experience. That said, Puerto Maldonado is not at all on the tourist trail. Public transport to Puerto Maldonado is infrequent, the city has very few tour operators and the hotels do not cater to tourists.
I traveled through Puerto Maldonado last year, on my way to Brazil.
Iquitos is known for it being the center of the Peruvian Amazon. So, it seems to make sense to focus your attention there.
Also, you are aware that both cities are about 1000km apart, as the crow flies?
Just to expand on a couple of the answers above, in logistical terms it's true that you have to fly to get to either Iquitos or Puerto Maldonado, but... it's worth noting that from Iquitos you can only really fly to Lima whereas you can fly between Puerto Maldonado and Cusco as well as Lima - this means that Puerto Maldonado fits in much better to a trip in the rest of Peru, assuming you also want to go and visit places like Machu Picchu.
Oh, and one more thing which may make the above irrelevant: if you want to see river dolphins it will have to be Iquitos: you don't get them in the southern Amazon basin!